Alisha Holloway, PhD
Assistant Professor
Epidemiology & Biostatistics
School of Medicine

Dr. Holloway’s research focuses on using comparative and population genomics to understand the evolution of mammalian traits and of gene regulatory networks in developing vertebrate hearts. Dr. Holloway is the founding director of the Gladstone Bioinformatics Core and directs a team of staff scientists who are experts in high-throughput data analysis and biostatistics. She also serves as Informatics Leader for the NHLBI Bench to Bassinet program, whose mission is to accelerate scientific discovery to clinical practice through collaborations of basic, translational and clinical research into congenital heart disease. In that role, she directs efforts to evaluate tools for high throughput sequence analysis, develop bioinformatics tools, and integrate analysis of orthogonal data sets.

• Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.
  Molecular biology and evolution 2015 Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS
• From scientific discovery to cures: bright stars within a galaxy.
  Cell 2015 Williams RS, Lotia S, Holloway AK, Pico AR
• motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.
  Statistics and its interface 2015 Kostka D, Friedrich T, Holloway AK, Pollard KS
• RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.
  Current protocols in human genetics 2014 Williams AG, Thomas S, Wyman SK, Holloway AK
• Long-read sequencing of chicken transcripts and identification of new transcript isoforms.
  PloS one 2014 Thomas S, Underwood JG, Tseng E, Holloway AK, Bench To Basinet CvDC Informatics Subcommittee
• A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.
  Genome biology 2013 Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N
• The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.
  Genome biology 2013 Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, …
• Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.
  Cell 2012 Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, …
• Genomic variation in natural populations of Drosophila melanogaster.
  Genetics 2012 Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ
• The microRNA expression changes associated with malignancy and SDHB mutation in pheochromocytoma.
  Endocrine-related cancer 2012 Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway AK, Krishna R, Nilubol N, Pacak K, Kebebew E
• A high-resolution map of human evolutionary constraint using 29 mammals.
  Nature 2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, …
• MiR-886-3p regulates cell proliferation and migration, and is dysregulated in familial non-medullary thyroid cancer.
  PloS one 2011 Xiong Y, Zhang L, Holloway AK, Wu X, Su L, Kebebew E
• Chromosomal haplotypes by genetic phasing of human families.
  American journal of human genetics 2011 Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF
• Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.
  PLoS genetics 2011 He BZ, Holloway AK, Maerkl SJ, Kreitman M
• Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.
  PloS one 2011 Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P
• Chromatin remodelling complex dosage modulates transcription factor function in heart development.
  Nature communications 2011 Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS…
• Identification of differentially expressed microRNA in parathyroid tumors.
  Annals of surgical oncology 2010 Rahbari R, Holloway AK, He M, Khanafshar E, Clark OH, Kebebew E
• Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster.
  Genetics 2010 Kolaczkowski B, Kern AD, Holloway AK, Begun DJ
• MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy.
  Cancer 2010 Patterson EE, Holloway AK, Weng J, Fojo T, Kebebew E
• Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences.
  Science (New York, N.Y.) 2010 Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E…
• Parathyroid neoplasms have distinct microRNA gene expression profile.
  Journal of the American College of Surgeons 2010 Reza Rahbari, Alisha K. Holloway, Mei He, Orlo H. Clark
• "Reverse ecology" and the power of population genomics.
  Evolution; international journal of organic evolution 2008 Li YF, Costello JC, Holloway AK, Hahn MW
• Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans.
  Genome biology 2008 Lawniczak MK, Holloway AK, Begun DJ, Jones CD
• Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.
  Genome research 2008 Holloway AK, Begun DJ, Siepel A, Pollard KS
• Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
  PLoS biology 2007 Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH
• Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster.
  Genetics 2007 Levine MT, Holloway AK, Arshad U, Begun DJ
• Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.
  PloS one 2007 Holloway AK, Begun DJ
• Adaptive gene expression divergence inferred from population genomics.
  PLoS genetics 2007 Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD
• Experimental evolution of gene duplicates in a bacterial plasmid model.
  Journal of molecular evolution 2007 Holloway AK, Palzkill T, Bull JJ
• The 2006 NESCent Phyloinformatics Hackathon: A Field Report.
  Evolutionary Bioinformatics 2007 Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne, William H. Piel,…
• Polyploids with different origins and ancestors form a single sexual polyploid species.
  The American naturalist 2006 Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM
• Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags.
  Genetics 2005 Begun DJ, Lindfors HA, Thompson ME, Holloway AK
• Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.
  Molecular biology and evolution 2004 Holloway AK, Begun DJ
• Difficulties in detecting hybridization.
  Systematic biology 2001 Holder MT, Anderson JA, Holloway AK
• Effective population size and genetic structure of a Piute ground squirrel (<i>Spermophilus mollis</i>) population.
  Canadian Journal of Zoology 2001 Michael F. Antolin, Beatrice Van Horne, Michael D. Berger, Jr., Alisha K. Holloway, Jennifer L. Roach, Ronald D. Weeks, Jr.
• Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population.
  Canadian Journal of Zoology 2001 Michael F Antolin, Beatrice Van Horne, Michael D Berger, Alisha K Holloway, Jennifer L Roach, Ronald D Weeks
• Garden sharing and garden stealing in fungus-growing ants.
  Die Naturwissenschaften 2000 Adams RM, Mueller UG, Holloway AK, Green AM, Narozniak J
• Linkage analysis of sex determination in Bracon sp. near hebetor (Hymenoptera: Braconidae).
  Genetics 2000 Holloway AK, Strand MR, Black WC, Antolin MF
• Survival of Diploid Males in Braconsp. near hebetor (Hymenoptera: Braconidae).
  Annals of the Entomological Society of America 1999 Alisha K. Holloway, George E. Heimpel, Michael R. Strand, Michael F. Antolin
• Role of local contractile activity and muscle fiber type on LPL regulation during exercise.
  The American journal of physiology 1998 Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway AK
• Relationship between numbers of the endangered American burying beetle Nicrophorus americanus Olivier (Coleoptera : Silphidae) and available food resources.
  Biological Conservation 1997 Alisha K. Holloway, Gary D. Schnell